Formed by sharing a pair of electrons between adjacent atoms
Chemical reactions requiring the most energy break and form covalent bonds
Electrostatic Interactions
Depend on electrical charge of atoms
Atoms with single opposite charges in water take ~6 kJ/mol to dissociate
Dielectric constant of water is very high, D = 80
Hydrogen Bonds
Interactions are also weak electrostatic interactions
Longer than covalent bonds
Energy of dissociation = ~4-13 kJ.mol
Hydrogen atom is shared between two electron negative atoms (nitrogen or oxygen)
One is the hydrogen bond donor (+), the other is the hydrogen bond acceptor (-)
van der Waal Interactions
Important in hydrophobic environments such as the interior of a molecule
depend on the distance between two atoms and non-symmetrical charge distribution around each
van der Waals contact distance is the point at which two atoms exhibit greatest attraction for each other
Too close and atoms repulse each other, but too far and the interaction is negligable
Contact point is approximately 2-3 Å
Energy of dissociation = ~2-4 kJ/mol
Water
Water affects non-covalent bonds which are important for biochemical reactions
Non-covalent interactions are important for biochemical reactions because they are easily reversible
Water is polar with asymmetric distribution of charge and highly cohesive through hydrogen bonding
High boiling point, heat of vaporization, heat of fusion, surface tension, internal cohesion, and dielectric constant
Excellent solvent for polar molecules
Hydrophilic Effect
High dielectric constant diminishes strength of electrostatic attractions between other polar molecules
Forms solvent (hydrated) shells around other polar molecules, creating new electrostatic fields
Rapid fluctuating hydrogen bond structure that allows other molecules to diffuse and interact
Allow high concentrations of other polar molecules to exist in water as a solution.
Hydrophobic Effect
Water interaction with non-polar molecules
Non-polar molecules aggregate together in water following the second law of thermodynamics to increase the total entropy of the system and release free energy
Hydrophobic effect promotes many biochemical reactions such as correct protein folding
Hydrophilic amino acids move towards the exterior
Hydrophobic amino acids move to the interior of the protein
Acids and Bases
Acid – H+ Donor
Strong acid produces a weak conjugate base – poor pH buffering
Weak acid produces a strong conjugate base – good pH buffering
Base – H+ Receiver
Strong base produces a weak conjugate acid – poor pH buffering
Weak base produces a strong conjugate acid – good pH buffering
Ka = Acid Equilibrium Constant
Ka = [H+][A-] / [HA]
[H+] remains constant when pH buffering is strong
pH
Logarithmic measure of the concentration of [H+]
pH = -log[H+]
Pure H2O at room temperature: [H+] equals [OH-] = 1 x 10-7 M
Therefore, -log[H+] = 7 and the pH of water is 7
pK
pK is the pH when the [conjugate acid] = [conjugate base]
Resistance to pH change is greatest (greatest buffering capacity)
pKa of an acid is the pH when [HA] = [A-]
Henderson-Hasselbalch Equation
Predicts the pH of a buffer by the –log [HA] / [A-]
For a weak acid, pH = pKa + log [A-] / [HA]
When [A-] equals [HA], the pH = pKa
Properties of a Buffer
Acid-base conjucate pair resists changes in pH of solution
Weak acid and strong conjugate base make a strong pH buffer
Bicarbonate buffer system in blood
Kidneys regulate H+ by renal excretion while lungs regulate CO2 by rate of ventilation
H+ + HCO3- <--> H2CO3 <--> H2O + CO2
Amino Acids
All proteins use the same set of 20 amino acids for the last several billion years
Amino acids vary in size, shape, charge, and chemical reactivity
Zwitterions (hybrid ions):
Amino acids in solution at physiological pH exist predominately as dipolar ions
Amine group is protonated (-NH3+)
Carboxyl group is deprotonated (-COO-)
Therefore, amino acid is fully ionized but electrically neutral
Amino acids are conjugate acid/base pairs (can be diprotic or tripotic depending on –R group)
Amino acid –R groups facilitate chemical reactions and form ionic bonds
All three pKa’s of the –COOH, -NH3+, and –R group determine the pI
pI is the isoelectric point which is the pH when the total net charge is zero
Amino acids at their isoelectric point will not move in an electric field.
Amino Acids have 4 different groups, (1) -NH3+, (2) –COO-, (3) –R group, (4) Hydrogen
Amino Acids are chiral and L-α-amino acids are constituents of proteins
Have an S (left) chiral configuration.
This is a Powerpoint slideshow with the amino acid structures (like flashcards) that Habib made in undergrad. Thought it might help someone:
Introduction to Proteins I
Dr. Kandice Williams, Ph.D.
Table of Contents
Covalent Bonds
Electrostatic Interactions
Hydrogen Bonds
van der Waal Interactions
Water
Hydrophilic Effect
Hydrophobic Effect
Acids and Bases
pH
pK
Henderson-Hasselbalch Equation
Properties of a Buffer
Amino Acids
Non-polar, aliphatic –R groups
Aromatic –R groups
Aliphatic hydroxyl –R groups
Aliphatic sulfhydral (thiol) –R group
Basic –R groups
Acidic –R groups and Uncharged derivatives
Non-Essential and Essential Amino Acids
Objectives